2017: A year in Precision Medicine in South Africa at CPGR and Artisan Biomed. What next?

In 2017, we took concrete steps into the Precision Medicine field in South Africa. I am saying this with some caution, for two reasons: firstly, Precision Medicine is an ambiguous term that means different things to different people; secondly, it’s one thing to talk about Precision Medicine in a place like London, UK, and a completely different one in Cape Town, South Africa; or in Enugu, Nigeria. Everything we do in this arena is guided by two essential questions: (i) in view of local context, can we deliver solutions that will be considered best-in-class anywhere; (ii) to what extent will these solutions work in (any) other African country?

With respect to the Precision Medicine definition, my own position is not to advocate blanket exome and genome sequencing to achieve some population health effect in the distant future. Rather, I’d argue that Precision Medicine is to deliver value to patients in precise amounts of time, information and volume. This doesn’t necessarily require access to information-rich testing for everyone; rather, it demands the ability to design, implement, execute and monitor processes that yield defined benefits for customers and end-users (patients).

My view is rather holistic, i.e. considering a whole patient journey as opposed to data generation in a laboratory only. I do think population health effects can be achieved but that will only happen on the basis of carefully designed interventions that are implemented on a broad basis; and, likely, not through organically grown activities because these will take long to show impact and, more importantly, will be plagued by variation where coherence and coordination is needed.

Also, I am not in a camp with people who think that genetic testing is a commodity that can be showered on people like manna from heaven. Such notions are fueled by technology providers, and adopters, who are quick to argue that genome sequencing is feasible at USD 1000,-. That may be true for some contexts but, usually, these aren’t taking into account any of the steps needed to collect samples, to analyse data, or to convert these into reports with a measure of clinical utility.

Then, there are those who think that genetic testing is simple, like a commodity that can be produced in factories and consumed with the morning paper over a cup of coffee. This is driven by an explosion of consumer-focused applications, many with dubious utility. For example, I think people should be free to spend their money on shawls printed from their DNA sequence; but, the proliferation of such offerings causes confusion in the public about what actual value can be derived from DNA analyses.

Lastly, to reduce Precision Medicine to the DNA level is a fallacy. I think the main reason why there is a current focus on genetic testing is because the technologies in use have been around for some time and are in a ready supply. That doesn’t mean, though, that all biological phenomena (medical conditions) can be explained by genetic traits. However, the flip-side of that argument is that a process and knowledge ecosystem can be created using molecular assays that are in broad use, thereby allowing the appropriation and diffusion of know-how when creating Precision Medicine solutions.

Coming back to our experience in the course of this year, this is what we have done and learned in a summarized fashion:

1. We have implemented a range of tests ranging from prenatal to postnatal testing, cancer (germline) and somatic tumour sequencing, to high-resolution HLA typing. We have been exome sequencing and just completed our first human genome. So, overall, we have been tackling a diversity of applications, with the concomitant ‘patient journey’ complexities. In total, we have completed in excess of 1000 tests in our first year of operation.

3. To support internal sample/data tracking, and across sites in Africa, we have started to implement a new LIMS. We went for an open source solution because it will allow more rapid capacity development at and integration of diverse sites in other African countries, considering resource limitations in many settings on the continent.

4. Streamlining sequence data processing, analysis and reporting has been a major focus this year. On the reporting side, we have started to work with SOPHiA GENETICS, a cloud-based solution that uses an Artificial Intelligence (AI) algorithm for variant interpretation and comes with access to a user community network to assist decision-making when interpreting genetic results. In parallel, we have been testing other solutions, putting a strong emphasis on the localisation (not necessarily internalization) of processes, data, and know-how.

5. To streamline secondary analysis, we have implemented a DRAGEN, an IT-powered processor purpose-built for secondary NGS data analysis. This has allowed us to increase scale and scope of routine and custom (project-based) Bioinformatics dramatically. Conversion of raw exome data into high-quality variant data-sets can now be done in a matter of minutes. This speeds up pipeline development and validation; and, it significantly reduces analysis and reporting turnaround time (TAT) where needed.

6. We have taken early steps in creating review panels, to develop, and improve, our offering against the perspectives of a group of multi-disciplinary experts. The aim here is two-fold: (i) to ensure that our testing solutions meet expectations and trust among our user base; (ii) to build external knowledge to develop Precision Medicine resources in (South) Africa.

7. We have started to explore new partnerships in order to make Precision Medicine more accessible and affordable in (South) Africa, notably in the field of stem cell typing for blood disorders (cancers, sickle cell disease). The initiative aims at creating value for (South) Africans but also for people of African descent, mainly by aggregating and utilizing data. In fact, it forms a template for making other high-end Precision Medicine solutions available to patients in (South) Africa through innovative fund-raising and data utilization models.

What is in store for 2018?

1. We will further streamline our data analysis pipelines, notably by integrating high-speed secondary data analysis (DRAGEN) with report generation. The aim will be to optimize existing processes to decrease TAT and increase automation, and therefore output standardization.

2. Using the above setup, we aim to increase collaborative efforts for the development of IT tools and Bioinformatics capacity, using a recently organised Hackathon as a template.

3. We will roll out new molecular applications, with a focus on complementing existing tests to create comprehensive ‘patient journey’ solutions. For example, linked to our HLA typing activities, we will offer ancestry profiling using high-density microarrays, as a means to facilitate the development of customized donor recruitment strategies in mixed ancestry populations.

4. For certain molecular applications, we will explore innovative new approaches to decrease the cost of goods, an antecedent to lowering the price of testing and enhancing access to patients in the public health sector in South Africa, and for out-of-pocket patients across the continent.

5. Process standardisation and verification will be one of our key focus areas. In scope, this will go beyond the accreditation of processes according to applicable ISO standards. It will seek to create consensus-based, consultative approaches to establishing best practice and fit-for-purpose Precision Medicine solutions in (South) Africa.

6. Building on existing projects and initiatives, we will further expand and build networks across Africa, with an aim to create value for individuals on the continent and of African descent. Among others, we will pilot HLA-typing programs with dedicated partner(s) on the continent, which in turn will form templates for other Precision Medicine activities.

7. We will grow our data aggregation and comprehension activities in order to leverage the digital information we are gathering into a diversity of value streams, seeking to establish platforms that will stimulate innovation and sustainability in developing Precision Medicine solutions in (South) Africa.